High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers

Abstract

The genetic diversity in Zanthoxylum species viz. Zanthoxylum nitidum, Zanthoxylum oxyphyllum and Zanthoxylum rhesta collected from the Upper Brahmaputra Valley Zone of Assam (NE India) was amplified using 13 random amplified polymorphic DNA (RAPD) markers and 9 inter-simple sequence repeat (ISSR) markers. RAPD markers were able to detect 81.82% polymorphism whereas ISSR detected 98.02% polymorphism. The genetic similarities were analyzed from the dendrogram constructed by RAPD and ISSR fingerprinting methods which divided the 3 species of Zanthoxylum into 3 clear different clusters. The principle component analysis (PCA) was carried out to confirm the clustering pattern of RAPD and ISSR analysis. Analysis of molecular variance (AMOVA) revealed the presence of significant variability between different Zanthoxylum species and within the species by both RAPD and ISSR markers. Z. nitidum was found to be sharing a high degree of variation with the other two Zanthoxylum species under study. The Nei's gene diversity (h), Shannon's information index (I), observed number of alleles (na) and effective number of alleles (ne) were also found to be higher in ISSR markers (0.3526, 0.5230, 1.9802 and 1.6145) than in RAPD markers (0.3144, 0.4610, 1.8182 and 1.5571). The values for total genotype diversity for among population (HT), within population diversity (Hs) and gene flow (Nm) were more in ISSR (0.3491, 0.2644 and 1.5610) than RAPD (0.3128, 0.2264 and 1.3087) but the mean coefficient of gene differentiation (GST) was more in RAPD (0.2764) than ISSR (0.2426). A comparison of this two finger printing methods was done by calculating MR, EMI and MI. The correlation coefficient between data matrices of RAPD and ISSR based on Mantel test was found to be significant (r = 0.65612).

Estimating Genetic Conformism of Korean Mulberry Cultivars Using Random Amplified Polymorphic DNA and Inter-Simple Sequence Repeat Profiling

“…The average PIC value using ISSR primers was found to be higher than those using RAPD primers. This outcome was in agreement with findings from Medhi et al (2014), who found high PIC values via ISSR during an analysis of the genetic diversity of Zanthoxylum species [24]. Taken together with other reports [4], our findings further suggest that ISSR primers can be used as potential markers for discriminating inter-species of Morus cultivars.…”

Inter simple sequence repeat markers to assess genetic diversity of the desert date (Balanites aegyptiaca Del.) for Sahelian ecosystem restoration

“…Indeed, AMOVA showed that 80% of the total genetic variations was attributed to variations within populations rather than between populations (G ST = 0.21). These findings are comparable to those reported by Alansi et al 14 in Z. spina-christi L. (G ST = 0.17) and Medhi et al 34 in Xanthoxylum spp. (G ST = 0.24).…”

Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper

“…2 ), how these processes shaped the current pattern of genetic variation within and between populations remains obscure. A range of previous studies attempted to study the genetic diversity of specific local varieties or species with molecular markers such as isozyme 14 , random amplified polymorphic DNA 15 , 16 , inter simple sequence repeat 15 , 17 , amplified fragment length polymorphism 18 , simple sequence repeat 19 – 22 , and chloroplast DNA 23 , 24 markers. The limited number of polymorphic loci produced by these low-resolution markers hinders genetic research on Zanthoxylum species.…”